Added BlueGene/Q Verlet cut-off scheme kernels, enhancements to CMake handling, support for bgclang (but latest compiler does not yet work with OpenMP), support for A2 core and QPX SIMD in CPU detection, updates to install guide.

Automated PP-PME (task) load-balancing: balancing non-bonded force and PME mesh workload when the two are executed on different compute-resources (i.e CPU and GPU or different CPUs). This enables GPU-CPU and PP-PME process load balancing by shifting work from the mesh to the non-bonded calculation.

PPPM/P3M with analytical derivative at the same cost and with the same features as PME.

New, advanced free energy sampling techniques.

AdResS adaptive resolution simulation support.

Enforced rotation ("rotational pulling")

Build configuration now uses CMake, configure+autoconf/make no longer supported. (The CMake build system features with a lot of automation and cleverness under the hood and we know that the it might not always prove to be as rock-solid as the old one. However, far more advanced and complex, so bear with us while we iron out issues that come up along the way.)

Improved regressiontests; these can now be run directly from the build tree using make check

g_hbond now utilizes OpenMP.

Bugfixes

No critical bugfixes. This version is based on 4.5.6 and all important fixes are "inherited" and therefore documented in the 4.5.6 release notes.

Changes that might affect your results

None for simulations set up with the traditional group cut-off scheme.

When switching from the group scheme to the Verlet scheme, integration of the equations of motion can get more accurate due to the exact cut-off treatment and buffering (this will, of course, depend on the original cut-off settings used). See the section Cut-off schemes for details.

Other important changes compared to 4.5

mdrun does now thread affinity setting

This means that when runing multiple mdrun processes on the same machine, one has to either provide a core "pin offset" using the -pinoffset command line option, or turn off internal affinities and take the performance hit (or alternatively manage affinities externally).

The choice of compiler matters more

With the switch to SIMD intrinsics, up-to-date SIMD CPU acceleration support, OpenMP, the compiler used matters more both in terms the ability to compile GROMACS correctly and from the point of view of mdrun performance. The recommended compilers that are known to work (=compile GROMACS correctly) and provide good performance on x86/AMD64 are: gcc 4.5 and later, Intel Compilers 12.0 and later and clang 3.1 (note the lack of OpenMP support which can cause 30%+ performance loss). In all cases you are strongly advised to use the most recent patch level available. GROMACS makes extensive use of compiler intrinsics to get the most out of your hardware, so if you use a compiler that is older than your hardware you are asking for trouble, because all the compilers have had bugs in their intrinsics implementations. For further details see ???.

completed removal of Fortran kernels (we are not aware of any systems where these would run faster than the corresponding non-accelerated C kernels by enough to be worth our effort, and probably the new force-only C kernels will be faster than the old Fortran kernels on any system where the disparity between Fortran and C compiler optimization is noticeable; speak up if any of this is a problem for you!)

completed removal of Power6 accelerated kernels (currently we lack the resources to implement accelerated kernels for Power architectures, and probably the new force-only C kernels will show results comparable with the old accelerated Power kernels; speak up if any of this is a problem for you - particularly if you have resources to offer to fix it!)